URL: BioWeka
Submitted by Martin Szugat;
posted on Tuesday, October 18, 2005 (1 comment)
BioWeka is a Java-based extension to the Weka framework for data mining [1], and like Weka it is licensed under the GPL. It adds the following functionality to the Weka framework:
- Loading FASTA, GenBank, EMBL and Swiss-Prot sequence files
- Loading XML files, e.g. MAGE-ML, ProML and InterProScan result sets
- Loading tab-delimited microarray data, e.g. TIGR, Stanford and Spot
- Classification based on BLAST or PSI-BLAST
- Classification based on alignments (local, global and secondary structure element)
- Classification of DNA/RNA sequences based on Eclat [2]
- Translation of sequences (DNA to RNA to Protein, DNA/RNA to its reverse complement)
- Generation of the open reading frames of DNA/RNA sequences
- Analysis of amino acid properties based on the Amino Acid Index database (AAindex)
- Calculation of codon frequencies or amino acid composition
- Normalization of numeric feature vectors
- Additional Weka utilities: Merge ARFF files, save ARFF files in a sequence format and create filter pipelines
Version 0.4 has just been released.
Feedback is welcome! Send it to
bioweka-users[at]lists.sourceforge.net.
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